Avengers Vs X-Men: Outbreak
by blacklotus21
Summary: In the aftermath of the Chitauri attack on New York, public opinion has turned against superheroes. The Avengers work tirelessly to regain public trust, resolve differences in their own ranks, and put their lives back together. When a mysterious biological threat emerges, the Avengers must find the source and stop it...before it's too late!
1. Chapter 1

Prologue: On the Horizon

Owning a bar in Alpine, Arizona was hard. Cathy Stern knew that better than anyone; she had been running the only one in town for as long as she could remember. Formerly a Mormon settlement, the town of Alpine and its residents had long rejected the need for any kind of bar. However, growing traffic and withering religious roots had led to a communal change of heart in the mid-20th century. Eager to start a venture, her great-grandfather had opened the Treetop Saloon, a small wooden establishment held together with rusty nails and entrepreneurial spirit. With time the salon grew into a bustling bar and diner, frequented by long-time residents and travelers on their way to the Arizona/New Mexico border.

"Micky's waiting on her beer, Jeff," Cathy barked at her employee as she balanced a full plate of food in each hand. With only 3 servers including herself, the Friday night rush was always a hassle. With a sigh, Cathy steadied the plate in her right hand and exited the kitchen. As she entered the main dining area, the sound of laughing, talking, and shouting brought a smile to her face. She rounded a row of bar stools and approached a line of tables, each one filled with boisterous patrons and local characters.

"Hey, Cathy!," one patron called as she set down the food she had been carrying. "Another round over here!"

"Gotcha Rick," she replied back, deftly dodging the flailing arm of a customer who had consumed one too many drinks. She made a beeline for the bar, but stopped abruptly as the bell hanging from the front door chimed.

Cathy sighed. The last thing she needed right now was another customer. Putting on a smile, she turned towards to greet her new patron.

"Welcome to the Treetop Bar and Grill! Why don't you find a place to . . . sit . . . ?"

The young boy in the doorway shrunk under her gaze, his face hiding under the hood of his frayed grey jacket. He shifted on one foot, one hand gripping the strap of his worn red backpack and the other buried in the pocket of what Cathy assumed used to be jeans. One leg had been torn off just above the knee, the other rolled up to be the same length.

Cathy tried to remember if she had ever seen the boy before. No, she would have remembered him. The kid seemed uncomfortable, almost nervous, as he lingered in the entrance of the bustling restaurant. Cathy guessed the boy was homeless, but where did he come from? Alpine was a small town; with less than 200 folks in town, it was easy to get to know everyone.

 _He probably got separated from his parents. It's pretty cold outside, he must have come in to warm up._

"Well hey there little guy," she greeted as she approached him with a smile. The child shrunk back into the doorway, and Cathy made an effort to appear casual. "What's going on?"

The boy raised his eyes to meet hers, and Cathy found herself momentarily lost in his strange reddish-brown gaze.

"Why don't you come in?" Cathy offered. "It's pretty chilly out there, but it's nice and toasty in here. Grab a seat." She gestured to an open booth by the window. "I'll get you a snack."

The boy stood silently, an unreadable expression plastered on his face as he looked over the inviting restauranteur. Finally, the kid padded over to the booth and removed his backpack. Placing it underneath the table, he slipped into the booth and removed his hood. He continued to eye her as she walked back to the kitchen.

"I've got Micky's beer," Jeff stated as he brushed past her on his way to the main dining room.

"Rick and his buddies want another round too," Cathy replied. "I'm cutting them off after this though. Lord knows how those boys are when they're shit-faced." The restauranteur peered her head into the kitchen. "Hey, get a burger going. And a Coke."

Ten minutes later, Cathy approached the booth where the silent child was sitting. Glued to the television over the bar, he didn't notice her until she set down the piping-hot hamburger and cold drink right in front of him.

"Here ya go buddy," she said with a smile. The boy's eyes fell from the television to the food, then to his host, then again to the food.

"Burger's not gonna hurt ya," Cathy assured. "Go ahead, dig in!" The boy eyed the meal warily for a few more seconds before picking it up and taking a small bite. Immediately, the child's widened, and a small smile crept broke through his clouded expression. Cathy chuckled as he took a larger, more eager bite, then another , then another. She watched silently as her young patron inhaled his food, pausing only to take sips of his drink.

"Good, huh?"

The boy emerged from his food and locked eyes with his host once more. He finished his bite before putting down the hamburger and shoving his hand into his pocket. Producing a beaten five-dollar bill, he offered it to her.

"Oh that's okay honey," Cathy said, shaking her head. "It's on the house."

The boy stood still for several moments before replacing the note and taking another bite of his meal. His eyes wandered back to the television. Cathy followed his gaze to the wall-mounted set, where a brunette newswoman sat beside a picture of several costumed crimefighters.

"… _anti-mutant sentiment on the rise, public outcry surrounding the X-Men school in Westchester, New York reached a head at a protest outside the institute's front gates. Renowned mutant rights activist and outed mutant Charles Xavier released a public statement…"_

"Those X-Men, huh?" Cathy commented. She looked down at the child in front of her, whose attention remained glued to the television. The boy took another massive bite of the burger, which by now was almost gone. "It's weird, having all these mutants running around with crazy powers and what not. Almost doesn't seem real, y'know."

If the child heard her, he gave no indication. He took another massive bite and watched as the newswoman began reporting on the weather.

"So, where are your parents, kiddo? You don't seem like you're from around here."

At her question, the boy's attention snapped back to his host. The child shrunk back into the booth, and his gaze fell. Cathy frowned.

 _Is he homeless?_

"You still hungry, kid?" Cathy asked, changing the subject. "Let me get you some desert."

"Who's the kid?" Jeff questioned as Cathy reentered the kitchen.

"Don't know," she answered. "He's not from around here. I don't think he's got any folks. No idea why he's up here in the middle of nowhere.

"Beats me. Maybe ask him? Either way, Rick and his buddies are getting rowdy. I think it's time they left."

"Sure," Cathy responded, grabbing a piece of pie from the counter. "Let me give this to the kid and I'll cut them off. Then we should call the cops. Make sure no one's looking for the squirt."

Pie in hand, Cathy emerged from the kitchen. She was surprised to find the boy's booth empty.

* * *

Emerging outside, the boy shuddered. The winter wind was biting, nipping at his ears and wracking his small frame. He put up his hood and tightened it with his jacket's frayed drawstrings. The child peered over his shoulder, and for a moment considered going back inside. It had been warm inside, and the woman had been nice . . . .

 _No_. _Adults always seem nice at first, but they always end up being mean. That lady was probably a real jerk who was just trying to trick me._

He started down the road, hoping to find his way back to the main drag. The meek light of nearby shops cast long shadows across the street that seemed to dance in the moonless night. The boy pulled at the drawstring of his jacket and steeled himself. A gripping terror welled in the pit of his stomach, but he forced himself to keep moving.

 _I'm too old to be scared of the dark. Captain America isn't scared of the dark, so I won't be either. There's nothing out here…_

A menacing, rumbling growl shattered the child's concentration. He swiveled around, surveying the area for the source of the sound. The street was empty.

 _There's…there's nothing out here. It must just be…there's nothing…_

But there was the noise again, echoing through the dimly lit streets. The child stood still and listened. A barely audible scratching sound drifted from the behind the boy. He swallowed the lump in his throat and turned around, his white-knuckled hands wrapped around his backpack straps.

Atop a nearby store, the kid spotted two yellow lights.

 _What's that?_

Curiosity overcoming his fear, the boy took a few tentative steps forward. Suddenly, the lights blinked, then narrowed. The boy realized that he was staring at a pair of eyes.

Without warning, a massive bipedal form rose atop the store, silhouetted in the moonlight. Its golden eyes remained locked on the quivering boy below. The creature gripped the front of the store sign with two massive arm-like appendages and leaned towards the child, a guttural growl rolling in its throat.

The boy screamed, turned, and ran.

Adrenaline pumping, the boy sprinted down the street back towards the diner. He peered over his shoulder, searching for any sign of the creature. Distracted as he was, the kid failed to notice the line of motorcycles in front of him. The child turned his attention forward just in time to collide with one of the motorbikes. The bike toppled, sending him sprawling onto the pavement. The he sat up and cradled his leg, panic momentarily forgotten. A thin line of blood dripped from a new gash in his knee.

Thoughts of the creature sparked new fear in the boy's mind. He struggled to his feet and looked around for any sign of his assailant. He saw no glowing eyes, no sign of any monster.

"What the fuck?"

The boy turned to find a young man looming over him, a bottle in one hand. A group of like-aged men stood in the diner's entrance, eyeing the fallen bike.

"What'd you do to . . . _hic_ . . . to my bike?!" The drunk man lumbered forward, causing the boy to stumble backward.

"C'mere you little shit," the man drawled. The boy turned around to run, only to have his drunken assailant wrap and arm around his torso and lift him off the group.

"What happened dude?" one of the men in the doorway asked.

"This little punk was messing with my bike," the drunk man replied, tightening his hold on the struggling child.

"What do we do with him?" a member of the group queried.

"I say we teach him a lesson," replied another.

"I'm down with that," a third chimed in.

The boy struggled in his captor's grip, tears pricking at the edges of his vision. Desperate to escape, he leaned forward and sank his teeth into the man's arm.

"Aaaarghh fuck!" the drunken patron exclaimed, loosening his hold on the child. The boy fell to the pavement, jumped up, and made a beeline for a nearby cluster of bushes.

"You okay Rick?"

"The fucker bit me!"

"Don't let him get away!"

The boy kept running, wincing at the throbbing pain in his knee. He hastily wiped away the tears clouding the edges of his vision and willed himself to stop crying. A bottle whizzed past his head and crashed into the blacktop, shattering into countless glimmering pieces. In a matter of seconds he reached the bushes. Diving behind them, he peered out at the street. Several of the group were approaching his hiding place. The rest had gathered around the fallen motorcycle.

None of them noticed the dark shape perched atop the diner's roof, it's glistening golden eyes fixed on the scene below.

The boy ran. Away from the men. Away from the town. Away from the monster.

Behind him, screaming pierced the quiet night.


	2. Gathering Storm

**Gathering Storm**

"Alright, move in!"

The S.H.I.E.L.D agents entered the Treetop Saloon one by one, guns raised. The hazmat-suit-clad team spread out as they filed in, surveying the eerily quiet establishment. The cool light of the midday sun illuminated the shards of the shattered front window, casting rays of light through the desecrated restaurant.

The agents moved deliberately, carefully avoiding the overturned chairs and shattered plates littering the room. One of them, the squad leader, raised his hand, signaling for the others to stop.

"Go check the back," he whispered to the soldier to his right. The agent nodded before carefully making his way to the kitchen and opening the door. Peering inside the pitch-black space, the soldier raised his weapon. He turned back to the leader of the group, silently confirming the order he had been given. Receiving a nod from his superior, the soldier turned and stepped into the darkness.

The soldier clicked on the flashlight attached to his gun and looked around. Half-finished meals sat on the counter, some of which had begun to attract flies. Pots and dishes were scattered haphazardly about the floor. Rounding a corner, the intrepid agent came to a halt. Viscera covered the wall in front of him, glimmering in the light.

The soldier tightened his grip on his weapon. He had been trained for this. Stay calm. Breach and clear.

A strange, garbled noise drew the agent's attention away from the gruesome scene. Swiveling to his right, the agent locked eyes with a woman standing behind a counter. The woman took rasping breaths as her gleaming, yellow eyes remained locked with his. The woman's veins seemed to pulsate beneath her pale, semi-translucent skin. The agent's raised his weapon

"Miss?" he asked. "Are…"

Without warning, the woman let out a guttural, gurgling cry and charged at the soldier. The agent reacted on instinct, firing a round into the mad woman's chest. She stumbled and let out an incoherent cry, but quickly recovered. Steeling himself, the soldier held down the trigger of his weapon, felling the mad woman in a hail of bullets.

He finished reloading his weapon just as the other agents burst into the room, guns raised and flashlights on.

"We heard shots," the leader stated.

"Contact," the soldier explained tersely. He shined his flashlight down at the woman's body and stepped back to avoid the rapidly forming pool of blood beneath his feet. "I'm fine."

"This is all just…Jesus," one of the agents chimed.

"Area seems clear commander," another added. "Orders?"

"Any survivors?" the commander asked.

"Negative," answered another member of the group

"Then head back to the staging area," the commander stated. "Ward is expecting a sit-rep."

* * *

It took the soldiers half an hour to reach their destination, a makeshift S.H.I.E.L.D. encampment on the outskirts of the town. Personnel mulled about, ducking in and out of the hastily constructed tents that served as temporary quarters, storage rooms, and medical facilities. The weary soldiers filed in to one of the medical tents, where they removed their gear and underwent decontamination procedures. Once cleared, most of the group headed towards their temporary quarters, eager to get some rest after a harrowing and exhausting morning.

The squad leader watched from the entrance of the medical tent as his men left, chatting and joking as they were wont to do. He silently wished to go with them. After spending the morning fighting…those _things_ …he was beginning to tire out. However, duty called. He would get some rest after making his report.

He soon found himself at the entrance to another tent. Ducking inside, the squad leader found a S.H.I.E.L.D agent seated at a table, frantically typing away at a laptop. Reports and charts covered the folding table serving as the agent's desk. The squad leader stood silently, watching his superior jot down notes in a document before taking a gulp from a water bottle a replacing it on the desk beside his computer.

"Commander Ward," the squad leader greeted with a salute. The seated gentleman's eyes lifted from his work and settled on the weary squad leader.

"Lieutenant Shepard," Ward replied, leaning back in his chair. "Your report,"

"Sir," Shepard responded. "We searched all building in sector eight. 24 contacts in total."

"Any survivors?" Ward questioned.

"No," replied Shepard, shifting on one foot. "One of my men had a particularly close encounter with an infected individual, but he says it didn't touch him. The CDC doctors cleared him when he got back to camp."

"I don't like all these CDC lab types meddling in our business," Ward stated, turning his attention to a report on his desk. "They're just more civilians for us to babysit."

Shepard hesitated for a moment before responding. "This _is_ their jurisdiction, sir."

Ward grunted as he typed a quick note on his laptop. "Hmph. That's what they said." The impatient commander picked up a paper on his desk and surveyed it. "You are dismissed, Lieutenant."

Shepard saluted silently before slipping out of the tent. Taking another drink of water, Ward put down the document he was holding and clicked a link on his laptop. A window with a rotating, segmented circle appeared onscreen, and Ward silently cursed being in the mountains. His phone reception had been shoddy all morning, and now his laptop was beginning to act up. Why couldn't S.H.I.E.L.D buy better equipment? He had hoped that the partnership with Stark Industries would remedy technological problems on the ground, but new tech had been less than forthcoming. If Stark was down here cleaning up the mess, Ward mused, maybe he would get off his ass and start fixing the problem.

Well, being a billionaire and a member of the Avengers had to have some perks.

Ward's laptop beeped, snapping him out of his train of thought. A woman's face appeared onscreen, her expression one of thinly veiled frustration.

"Director Hill," Ward greeted.

"What's the status on the ground?" Director Hill queried, dispensing with the pleasantries.

"We've completed our search of the town. No survivors. Just monsters.

Hill grimaced. "An entire town dead almost overnight. Shit." The normally composed woman leaned back and frowned as she skimmed a report on her desk.

"Two weeks. Two towns gone overnight. And we're still not even close to containing this."

"We've cut off access to and from Alpine," Ward commented. "We set up a perimeter around the town, and a second perimeter 5 miles outside that. We've diverted all traffic; so far no one seems to suspect anything."

"Good," Hill replied. "We need to make sure this stays secret until we contain it. Word of this gets out, we'll have a PR nightmare on our hands. Any developments on the CDC's end?"

"Nope," Ward answered. "They keep saying that it's unlike any disease they've ever seen. Apparently, no one knows what it is or how to treat it."

Director Hill shook her head. "We've been tracking the spread of the infection. The towns hit so far have followed a line heading East. Whatever's doing this is on the move. We need to find it and contain it before it reaches a more populated area."

"But without any survivors, we have no leads," Ward added.

Director Hill's expression darkened. "But we do know one thing. This disease can't be natural. Someone set this up. Someone with the resources and intelligence to engineer a threat that we don't have an answer to."

The S.H.I.E.L.D. director stopped for a moment, eyeing her subordinate intently. After a moment, her demeanor relaxed, and she turned away from the screen.

"Get back to work Commander. I have to make a call."

* * *

A young boy leaned forward as he dug around in his beaten red backpack. After a moment, his eyes lit up and he withdrew a wrapped granola bar. Placing the snack at his side, the boy plunged his hand into the satchel once more, this time retrieving a box of band-aids and a scratched canteen. He opened the box and silently thanked his luck upon finding one Captain America bandage left.

The boy closed his backpack and scooted over to the open door of the boxcar he was occupying. The wind gusted by, whipping up his disheveled hair and chilling his hands. He huddled into himself and stepped away from the windy door of the car.

Stretching out, the child unwrapped the bandage and carefully applied it to the cut on his knee. It wasn't hurting too bad anymore, but he had heard somewhere that not putting a band-aid on a cut could make it worse.

Satisfied with his handiwork, the boy scooted over to the open door of the boxcar he was occupying, sat down cross-legged, and unwrapped his food. For a few quiet minutes, he munched on the somewhat stale granola bar and watched the mountains and forest rush by.

This was definitely the prettiest place he had ever seen. He hadn't been to a lot of places, but this one had a lot more trees than the other places he had been. He liked the green. He liked the cool, fresh air. He liked the quiet. Maybe he could find a place like this to live. A place where no one would hit him or throw bottles at him. Where the monster couldn't get him.

The child's expression grew serious. He hadn't seen the monster since that nice lady had given him food a couple days ago. He hoped that the train would take him as far away from that _thing_ as possible. Then, he would…um…

…what _would_ he do?

Running and hiding hadn't given him much time to think of a next move. Maybe he'd find his parents somewhere.

 _Wait, do I have parents? I have to, right...? They're probably looking for me..._

Leaning back, the boy rested his head on his backpack. Right now, all he wanted to do was take a nap. He'd figure out a plan later. Reaching back, the boy unzipped his backpack and pulled out a faded, blue blanket. Snuggling into the blanket, the kid turned onto his side and fell into a fitful sleep.

* * *

"You summoned me, Charles?" Dr. McCoy asked as he entered the X-Mansion's owner's private study. Looking up from the titillating novel he had been reading, the professor smiled and marked his place before setting down the book on the coffee table.

"Yes, Hank. I hope I haven't interrupted anything important."

"Nothing that can't wait," the fuzzy doctor responded.

"Good," Professor Xavier said, "because I have an errand for you to run."

"Oh?" McCoy exclaimed.

"While using Cerebro this afternoon, I located a new mutant signature in Arizona. I've been tracking it for the better part of the afternoon. I was hoping you might locate the mutant and bring it back to the Institute.

"What have you learned about this mysterious mutant?" McCoy asked.

"Very little, I'm afraid," Charles responded. "I was hoping you might be able to uncover some clues as to the nature of this elusive character. After all, you have proven yourself to be a capable detective. Though, I caution you to be discreet. In light of recent events, I feel that it would be in our best interest to exercise a degree of…"

"…subtlety." McCoy finished.

"Precisely," Charles replied. "When can you leave?"

"I shall depart posthaste," Dr. McCoy stated.

"I will input the coordinates into the Blackbird," Xavier said, following his mutant colleague out of the study. "Good luck, and be careful."


End file.
